RMSD Matrix calculation module
Submodules
Module contents
RMSD matrix module.
This module calculates of the RMSD matrix between all the models generated in the previous step.
As all the pairwise RMSD calculations are independent, the module distributes them over all the available cores in an optimal way.
Once created, the RMSD matrix is saved in text form in the current rmsdmatrix folder. The path to this file is then shared with the following step of the workflow by means of the json file rmsd_matrix.json.
The module accepts two parameters in input, namely:
max_models (default = 10000)
resdic_ : an expandable parameter to specify which residues must be considered for the alignment and the RMSD calculation. If there are two proteins denoted by chain IDs A and B, then the user can operate such selection in the following way inside the configuration file
>>> resdic_A = [1,2,3,4]
>>> resdic_B = [2,3,4]
thus telling the module to consider residues from 1 to 4 of chain A and from 2 to 4 of chain B for the alignment and RMSD calculation.
- class haddock.modules.analysis.rmsdmatrix.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/analysis/rmsdmatrix/defaults.yaml'))[source]
Bases:
BaseHaddockModule
HADDOCK3 module for clustering with RMSD.